New variant report 2020-12-27
Data source and processing
All whole genome SARS-CoV-2 sequences were pulled from GISAID at 2020-12-27 12:19 GMT. The genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.
The sequences were then assigned lineages with pangolin v2.1.3, pangoLEARN version 2020-12-17.
Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs (defined here and B.1.351 to any sequences with more than 3 of the 5 defining B.1.351 SNPs.
Table 1 | Summary of data
| Lineage | Country | Sequence count | Earliest sequence | Travel history |
|---|---|---|---|---|
| B.1.351 | South_Africa 259, UK 1 | 260 | 2020-10-08 | |
| B.1.1.7 | UK 4249, Italy 11, Denmark 9, Ireland 7, Netherlands 3, Australia 3, Hong_Kong 2, Singapore 1, Israel 1, France 1 | 4287 | 2020-09-20 |
Lineage B.1.351
Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.
Table B.1.351 | Lineage B.1.351
| Statistic | Information |
|---|---|
| Count | 260 |
| Likely origin | South Africa |
| SNPs | aa:orf1ab:K1655N aa:S:D215G aa:S:E484K aa:S:N501Y snp:C23664T |
Figure 1 | Cumulative sequence count over time B.1.351
Figure 2 | Date of earliest B.1.351 detected
Figure 3 | Map of B.1.351 sequence counts
Figure 4 | Sequence count per country B.1.351
Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country
Lineage B.1.1.7
Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.
Table B.1.1.7 | Lineage B.1.1.7
| Statistic | Information |
|---|---|
| Count | 4287 |
| Likely origin | United Kingdom |
| SNPs | aa:orf1ab:T1001I aa:orf1ab:A1708D aa:orf1ab:I2230T del:11288:9 del:21765:6 del:21991:3 aa:S:N501Y aa:S:A570D aa:S:P681H aa:S:T716I aa:S:S982A aa:S:D1118H aa:Orf8:Q27* aa:Orf8:R52I aa:Orf8:Y73C aa:N:D3L aa:N:S235F |
Figure 6 | Cumulative sequence count over time B.1.1.7
Figure 7 | Date of earliest B.1.1.7 detected
Figure 8 | Map of B.1.1.7 sequence counts
Figure 9 | Sequence count per country B.1.1.7
Figure 10 | Frequency B.1.1.7 in sequences produced since first new variant reported per country
Figure 11 | Air traffic from UK by destination
The number of ticketed origin-to-destination journeys from London airports to countries outside the United Kingdom during October 2020.
Colours indicate numbers of published genomes of B.1.1.7 deposited on GISAID as of December 26, 2020. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.1.7 sequences on GISAID as of the 26-Dec-2020. White bars indicate countries with no reports of B.1.1.7.
Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.
Figure by Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer
